{"id":636,"date":"2013-06-20T12:46:09","date_gmt":"2013-06-20T20:46:09","guid":{"rendered":"http:\/\/www.kylemathewson.com\/?p=636"},"modified":"2013-06-20T12:46:09","modified_gmt":"2013-06-20T20:46:09","slug":"cnl-virtualbox-setup","status":"publish","type":"post","link":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/cnl-virtualbox-setup\/","title":{"rendered":"CNL VirtualBox Setup"},"content":{"rendered":"
\n

Ok so I have no, with Antoine’s excellent help, setup the virtual linux machine on Arch4. <\/p>\n

Once you are setup, a shared folder will exist between \/bi-cnl-arch4\/data\/freesurfer and \/home\/cnl\/freesurfer<\/p>\n<\/blockquote>\n

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This is the freesurfer director in ubuntu, DONT CLUTTER IT UP WITH OTHER STUFF!!!!!<\/p>\n<\/blockquote>\n

\n

You should be able to log into Arch4 remotely or in person on your account.<\/p>\n

At this time you should see an icon on the desktop <\/p>\n

\"image\"<\/a><\/p>\n

This will pop up: You need to find and load the disk image that we all share by following these instructions:<\/p>\n

\"image\"<\/a><\/p>\n

Click New: \"image\"<\/a><\/p>\n<\/blockquote>\n

Now fill in the name for this disk, Ubuntu64_[your username], the rest should fill in automatically, press next<\/p>\n

\"image\"<\/a><\/p>\n

Change the RAM amount to 2048 and press next<\/p>\n

\"image\"<\/a><\/p>\n

Use an existing virtual hard drive file, click the folder, and go to Ubuntu64.vdi<\/p>\n

\"image\"<\/a><\/p>\n

Now click settings, \"image\"<\/a><\/p>\n

Shared Folders, Add new icon \"image\"<\/a><\/p>\n

\"image\"<\/a><\/p>\n

Select the freesurfer C:\/data\/freesurfer folder and select automount, then press Ok> OK<\/p>\n

<\/p>\n

\"image\"<\/a><\/p>\n

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Now press start, it will open the virtual linux OS<\/p>\n

\"image\"<\/a><\/p>\n

Login as CNL, no password<\/p>\n

\"image\"<\/a><\/p>\n

Maximize the window to make it full screen if you like<\/p>\n

***BEFORE YOU DO ANYTHING ELSE, setup the environment by running the terminal:<\/p>\n

On the left side, open a terminal<\/p>\n

\"image\"<\/a><\/p>\n

Type the CNL password XXXXXXXXX:<\/p>\n

\"image\"<\/a><\/p>\n

Now you are ready to go..<\/p>\n

type tksurfer 1501 lh inflated for example to see the inflated brain of subject 1501<\/p>\n

You can also use AFNI from this terminal,<\/p>\n

just type <\/p>\n

\"image\"<\/a><\/p>\n

All of the AFNI, FSL, and freesurfer commands should work from the command line<\/p>\n

You can use the FSL viewer here to see any of your .nii files<\/p>\n

\"image\"<\/a><\/p>\n<\/blockquote>\n","protected":false},"excerpt":{"rendered":"

Ok so I have no, with Antoine’s excellent help, setup the virtual linux machine on Arch4. Once you are setup, a shared folder will exist between \/bi-cnl-arch4\/data\/freesurfer and \/home\/cnl\/freesurfer This is the freesurfer director in ubuntu, DONT CLUTTER IT UP WITH OTHER STUFF!!!!! You should be able to log into Arch4 remotely or in person … <\/p>\n

Continue reading “CNL VirtualBox Setup”<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-636","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/posts\/636","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/comments?post=636"}],"version-history":[{"count":0,"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/posts\/636\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/media?parent=636"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/categories?post=636"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.psych.ualberta.ca\/kylemathewson\/wp-json\/wp\/v2\/tags?post=636"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}